| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
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| 5. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 6. |
- Sampson, Joshua N., et al.
(author)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
-
Journal article (peer-reviewed)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 7. |
- Tang, Ting-Ting, et al.
(author)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Journal article (peer-reviewed)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 8. |
- Wang, Zhaoming, et al.
(author)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 9. |
- Zhu, Zhen-Long, et al.
(author)
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Cytoplasmic expression of p33(ING1b) is correlated with tumorigenesis and progression of human esophageal squamous cell carcinoma.
- 2013
-
In: Oncology letters. - : Spandidos Publications. - 1792-1074 .- 1792-1082. ; 5:1, s. 161-166
-
Journal article (peer-reviewed)abstract
- p33(ING1b), a newly discovered candidate tumor suppressor gene and a nuclear protein, belongs to the inhibitor of growth gene family. Previous studies have shown that p33(ING1b) is involved in the restriction of cell growth and proliferation, apoptosis, tumor anchorage-independent growth, cellular senescence, maintenance of genomic stability and modulation of cell cycle checkpoints. Loss of nuclear p33(ING1b) has been observed in melanoma, seminoma, papillary thyroid carcinoma, oral squamous cell carcinoma, breast ductal cancer and acute lymphoblastic leukemia. Inactivation and/or decreased expression of p33(ING1b) have been reported in various types of cancer, including head and neck squamous cell, breast, lung, stomach, blood and brain malignancies. Since little is known about the clinicopathological significance of p33(ING1b) in esophageal squamous cell carcinoma (ESCC), this study aimed to investigate the association of p33(ING1b) expression with clinicopathological variables and particularly interesting new cysteine-histidine rich protein (PINCH) in patients with ESCC. p33(ING1b) expression was examined by immunohistochemistry in 20 normal esophageal mucosa and in 64 ESCC specimens. The results revealed that the positive expression of p33(ING1b) protein in normal squamous cells was localized in the nucleus alone and the positive rate was 95%, while in ESCCs, the positive expression was mainly in the cytoplasm, together with nuclear expression, and the positive rate was 36% (P<0.0001). Furthermore, the cases with lymph node metastasis showed a higher frequency of positive cytoplasmic expression than those without metastasis (P=0.001). The cytoplasmic expression of p33(ING1b) was positively related to PINCH expression (P<0.0001) in ESCC, and the cases positive for both proteins had a high lymph node metastasis rate (P=0.001). In conclusion, p33(ING1b) cellular compartmental shift from the nucleus to the cytoplasm may cause loss of normal cellular function and play a central role in the tumorigenesis and metastasis of ESCC.
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| 10. |
- Zhu, Zhen-Long, et al.
(author)
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PINCH expression and its clinicopathological significance in gastric adenocarcinoma
- 2012
-
In: Disease Markers. - : IOS Press. - 0278-0240 .- 1875-8630. ; 33:4, s. 171-178
-
Journal article (peer-reviewed)abstract
- Objective: Particularly interesting new cysteine-histidine rich protein (PINCH) is an important component of the local adhesion complexes and upregulated in several types of malignancies, and involved in the incidence and development of tumours. PINCH expression is also independently correlated with poorer survival in patients with colorectal cancer. However, there is no study of PINCH in gastric cancer, therefore, the aim of this project was to investigate PINCH expression and its clinicopathological significance in gastric adenocarcinoma. less thanbrgreater than less thanbrgreater thanPatients and methods: PINCH expression was immunohistochemically examined in normal gastric mucous (n = 30) and gastric adenocarcinoma (n = 73), from gastric cancer patients. less thanbrgreater than less thanbrgreater thanResults: PINCH expression in the associated-stroma of gastric cancers was heterogeneous, and its positive rate (75%) was higher than that of normal gastric mucosa (43%, X-2 = 9.711, p = 0.002). The stronger staining was observed at the invasive edge of tumour when compared to the inner area of tumour. The rate of positive PINCH (88%) in the cases with lymph node metastasis was higher than that (52%) in the cases without metastasis (X-2 = 11.151, p = 0.001). PINCH expression was not correlated with patients gender, age, tumour size, differentiation and invasion depth (p andgt; 0.05). less thanbrgreater than less thanbrgreater thanConclusion: PINCH protein might play an important role in the tumourigenesis and metastasis of gastric adenocarcinoma.
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| 11. |
- Jin, Ying-Hui, et al.
(author)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
-
In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
-
Journal article (peer-reviewed)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 12. |
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| 13. |
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| 14. |
- Schuettpelz, Eric, et al.
(author)
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A community-derived classification for extant lycophytes and ferns
- 2016
-
In: Journal of Systematics and Evolution. - : Wiley. - 1674-4918 .- 1759-6831. ; 54:6, s. 563-603
-
Journal article (peer-reviewed)abstract
- Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.
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| 15. |
- Wang, Min, et al.
(author)
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Apolipoprotein M induces inhibition of inflammatory responses via the S1PR1 and DHCR24 pathways
- 2019
-
In: Molecular Medicine Reports. - 1791-2997. ; 19:2, s. 1272-1283
-
Journal article (peer-reviewed)abstract
- © 2019 Spandidos Publications. All rights reserved. Apolipoprotein M (ApoM) is a type of apolipoprotein. It is well known that high-density lipoprotein (HDL) decreases inflammatory responses via the apoM-sphingosine-1-phosphate (S1P) pathway. The present study further investigated the importance of ApoM in the inhibitory effects of HDL on inflammation. Mice with an apoM gene deficiency (apoM-/-) were employed to investigate the effects of ApoM on the expression of interleukin-1β (IL-1β), monocyte chemotactic protein-1 (MCP-1), S1P receptor-1 (S1PR1) and 3β-hydroxysterol Δ-24-reductase (DHCR24), as compared with in wild-type mice (apoM+/+). Furthermore, cell culture experiments were performed using a permanent human hybrid endothelial cell line (EA.hy926). Cells were cultured in the presence of recombinant human apoM (rec-apoM) or were induced to overexpress apoM (apoMTg); subsequently, cells were treated with tumor necrosis factor-α (TNF-α), in order to investigate the effects of ApoM on IL-1β and MCP-1. The results demonstrated that the mRNA expression levels of IL-1β and MCP-1 were significantly higher in the liver following administration of lipopolysaccharide in apoM-/- mice compared with in apoM+/+ mice. In cell culture experiments, when cells were pre-cultured with rec-apoM or were engineered to overexpress apoM (apoMTg), they exhibited decreased expression levels of IL-1β and MCP-1 following TNF-α treatment compared with in normal apoM-expressing cells (apoMTgN). Furthermore, the mRNA expression levels of IL-1β and MCP-1 were significantly elevated following addition of the S1PR1 inhibitor W146, but not by the scavenger receptor class B type I inhibitor, block lipid transport-1 (BLT-1), in apoMTg cells prior to TNF-α treatment. Conversely, there were no differences in these inflammatory biomarkers under the same conditions in apoMTgN cells. The mRNA expression levels of DHCR24 were significantly reduced by the addition of BLT-1 prior to TNF-α treatment in apoMTg cells; however, there was no difference in the expression of this inflammatory biomarker in apoMTgN cells. In conclusion, ApoM displayed inhibitory effects against the inflammatory response in vivo and in vitro; these effects may be induced via the S1PR1 and DHCR24 pathways.
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| 16. |
- Zhu, Zhen-Long, et al.
(author)
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Overexpression of FXYD-3 is involved in the tumorigenesis and development of esophageal squamous cell carcinoma
- 2013
-
In: Disease Markers. - : IOS Press. - 0278-0240 .- 1875-8630. ; 35:3, s. 195-202
-
Journal article (peer-reviewed)abstract
- Objective: To investigate the association of FXYD-3 expression with clinicopathological variables and PINCH in patients with ESCC.Patients and methods: Expression of FXYD-3 protein was immunohistochemically examined in normal esophageal mucous (n = 20) and ESCC (n = 64). Results: Expression of FXYD-3 in the cytoplasm markedly increased from normal esophageal epithelial cells to primary ESCC ( p = 0.001). The expression of FXYD-3 was correlated with TNM stages and depth of tumour invasion. Furthermore, the cases with lymph node metastasis tended to show a higher frequency of positive expression than those without metastasis ( p = 0.086), and FXYD-3 expression tended to be positively related to the expression of PINCH (p = 0.063). Moreover, the cases positive for both proteins had the highest frequency of lymph node metastasis (p = 0.001). However, FXYD-3 expression was not correlated with patient,s gender (p = 0.847), age (p = 0.876), tumour location (p = 0.279), size (p = 0.771) , grade of differentiation (p = 0.279), and survival (p = 0.113).Conclusion: overexpression of FXYD-3 in the cytoplasm may play an important role in the tumourigenesis and development in the human ESCC, particularly in combination with PINCH expression.
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| 17. |
-
- 2019
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Journal article (peer-reviewed)
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| 18. |
- Aaltonen, T., et al.
(author)
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Tevatron Run II combination of the effective leptonic electroweak mixing angle
- 2018
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:11
-
Journal article (peer-reviewed)abstract
- Drell-Yan lepton pairs produced in the process p (p) over bar -> l(+)l(-) + X through an intermediate gamma*/Z boson have an asymmetry in their angular distribution related to the spontaneous symmetry breaking of the electroweak force and the associated mixing of its neutral gauge bosons. The CDF and D0 experiments have measured the effective-leptonic electroweak mixing parameter sin(2) theta(lept)(eff) using electron and muon pairs selected from the full Tevatron proton-antiproton data sets collected in 2001-2011, corresponding to 9-10 fb(-1) of integrated luminosity. The combination of these measurements yields the most precise result from hadron colliders, sin(2)theta(lept)(eff) = 0.23148 +/- 0.00033. This result is consistent with, and approaches in precision, the best measurements from electron-positron colliders. The standard model inference of the on-shell electroweak mixing parameter sin(2) theta(W), or equivalently the W-boson mass M-W, using the ZFITTER software package yields sin(2) theta(W) = 0.22324 +/- 0.00033 or equivalently, M-W = 80.367 +/- 0.017 GeV/c(2).
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| 19. |
- Calabrese, Claudia, et al.
(author)
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Genomic basis for RNA alterations in cancer
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
-
Journal article (peer-reviewed)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 20. |
- Cavka, Adnan, et al.
(author)
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Production of bacterial cellulose and enzyme from waste fiber sludge
- 2013
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In: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834. ; 6:25
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Journal article (peer-reviewed)abstract
- Background: Bacterial cellulose (BC) is a highly crystalline and mechanically stable nanopolymer, which has excellent potential as a material in many novel applications, especially if it can be produced in large amounts from an inexpensive feedstock. Waste fiber sludge, a residue with little or no value, originates from pulp mills and lignocellulosic biorefineries. A high cellulose and low lignin content contributes to making the fiber sludge suitable for bioconversion, even without a thermochemical pretreatment step. In this study, the possibility to combine production of BC and hydrolytic enzymes from fiber sludge was investigated. The BC was characterized using field-emission scanning electron microscopy and X-ray diffraction analysis, and its mechanical properties were investigated.Results: Bacterial cellulose and enzymes were produced through sequential fermentations with the bacterium Gluconacetobacter xylinus and the filamentous fungus Trichoderma reesei. Fiber sludges from sulfate (SAFS) and sulfite (SIFS) processes were hydrolyzed enzymatically without prior thermochemical pretreatment and the resulting hydrolysates were used for BC production. The highest volumetric yields of BC from SAFS and SIFS were 11 and 10 g/L (DW), respectively. The BC yield on initial sugar in hydrolysate-based medium reached 0.3 g/g after seven days of cultivation. The tensile strength of wet BC from hydrolysate medium was about 0.04 MPa compared to about 0.03 MPa for BC from a glucose-based reference medium, while the crystallinity was slightly lower for BC from hydrolysate cultures. The spent hydrolysates were used for production of cellulase with T. reesei. The cellulase activity (CMCase activity) in spent SAFS and SIFS hydrolysates reached 5.2 U/mL (87 nkat/mL), which was similar to the activity level obtained in a reference medium containing equal amounts of reducing sugar.Conclusions: It was shown that waste fiber sludge is a suitable raw material for production of bacterial cellulose and enzymes through sequential fermentation. The concept studied offers efficient utilization of the various components in fiber sludge hydrolysates and affords a possibility to combine production of two high value-added products using residual streams from pulp mills and biorefineries. Cellulase produced in this manner could tentatively be used to hydrolyze fresh fiber sludge to obtain medium suitable for production of BC in the same biorefinery.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Chen, Yu-Xiang, et al.
(author)
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Selective translation by alternative bacterial ribosomes
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:32, s. 19487-19496
-
Journal article (peer-reviewed)abstract
- Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain of M. smegmatis in which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.
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| 25. |
- Fan, Jin, et al.
(author)
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Development of wideband orthomode transducers for FAST cryogenic receiver system
- 2020
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In: Research in Astronomy and Astrophysics. - : IOP Publishing. - 1674-4527. ; 20:5
-
Journal article (peer-reviewed)abstract
- This paper describes the design, construction, and performance of the wideband orthomode transducers (OMTs) for the L- (1.2-1.8 GHz), the S- (2-3 GHz) and the P- (0.56-1.12 GHz) band receiver systems of the Five-hundred-meter Aperture Spherical radio Telescope (FAST). These OMTs operate at the cryogenic temperature of 70K to reduce their thermal noise contribution to the receiver chains. The development on the FAST L- and S-band quad-ridged waveguide (QRWG) OMTs is carried out based on the theoretical mode analysis. In view of the miniaturization of FAST cryogenic receiver system at P-band, a novel wideband compact bowtie dipole OMT is designed with an octave bandwidth as well as a length of only quarter wavelength. The proposed L-, S- and P-band OMTs are designed and optimized by using Ansys High Frequency Structure Simulator (HFSS), and then manufactured, tested at room temperature. Measurement of FAST cryogenic receiver system noise is also performed with the L-, S- and P-band OMTs installed. The measured results fully comply with the design specifications.
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| 26. |
- Gao, Xiang, et al.
(author)
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Planting Age Identification and Yield Prediction of Apple Orchard Using Time-Series Spectral Endmember and Logistic Growth Model
- 2023
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In: Remote Sensing. - : MDPI AG. - 2072-4292. ; 15:3, s. 642-642
-
Journal article (peer-reviewed)abstract
- In response to significant shifts in dietary and lifestyle preferences, the global demand for fruits has increased dramatically, especially for apples, which are consumed worldwide. Growing apple orchards of more productive and higher quality with limited land resources is the way forward. Precise planting age identification and yield prediction are indispensable for the apple market in terms of sustainable supply, price regulation, and planting management. The planting age of apple trees significantly determines productivity, quality, and yield. Therefore, we integrated the time-series spectral endmember and logistic growth model (LGM) to accurately identify the planting age of apple orchard, and we conducted planting age-driven yield prediction using a neural network model. Firstly, we fitted the time-series spectral endmember of green photosynthetic vegetation (GV) with the LGM. By using the four-points method, the environmental carrying capacity (ECC) in the LGM was available, which serves as a crucial parameter to determine the planting age. Secondly, we combined annual planting age with historical apple yield to train the back propagation (BP) neural network model and obtained the predicted apple yields for 12 counties. The results show that the LGM method can accurately estimate the orchard planting age, with Mean Absolute Error (MAE) being 1.76 and the Root Mean Square Error (RMSE) being 2.24. The strong correlation between orchard planting age and apple yield was proved. The results of planting age-driven yield prediction have high accuracy, with the MAE up to 2.95% and the RMSE up to 3.71%. This study provides a novel method to accurately estimate apple orchard planting age and yields, which can support policy formulation and orchard planning in the future.
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| 27. |
- Guo, Xiang, et al.
(author)
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Comparison of methods for detoxification of spruce hydrolysate for bacterial cellulose production
- 2013
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In: Microbial Cell Factories. - : BioMed Central. - 1475-2859. ; 12
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Bacterial cellulose (BC) is a nanostructured material with unique properties and wide applicability. In order to decrease the production cost of bacterial cellulose, lignocellulose-based media have considerable potential as alternative cost-effective feedstocks. However, pretreatment and enzymatic hydrolysis of lignocellulose to sugars also generate fermentation inhibitors. Detoxification of lignocellulosic hydrolysates is needed to achieve efficient production of BC. In this investigation, different methods for detoxification of spruce hydrolysate prior to production of BC were compared with respect to effects on potential inhibitors and fermentable sugars, sugar consumption, BC yield, and cell viability. The objectives were to identify efficient detoxification methods and to achieve a better understanding of the role played by different inhibitors in lignocellulosic hydrolysates.RESULTS: In a first series of experiments, the detoxification methods investigated included treatments with activated charcoal, alkali [sodium hydroxide, calcium hydroxide (overliming), and ammonium hydroxide], anion and cation ion-exchange resins, and reducing agents (sodium sulfite and sodium dithionite). A second series of detoxification experiments included enzymatic treatments (laccase and peroxidase). The potential inhibitors studied included aliphatic acids, furan aldehydes, and phenolic compounds. The best effects in the first series of detoxification experiments were achieved with activated charcoal and anion exchanger. After detoxification with activated charcoal the BC yield was 8.2 g/L, while, it was 7.5 g/L in a reference medium without inhibitors. Treatments with anion exchanger at pH 10 and pH 5.5 gave a BC yield of 7.9 g/L and 6.3 g/L, respectively. The first series of experiments suggested that there was a relationship between the BC yield and phenolic inhibitors. Therefore, the second series of detoxification experiments focused on treatments with phenol-oxidizing enzymes. The BC yield in the laccase-detoxified hydrolysate reached 5.0-5.5 g/L after 14 days cultivation, which demonstrated the important inhibitory role played by phenolic compounds.CONCLUSIONS: The investigation shows that detoxification methods that efficiently remove phenolics benefit bacterial growth and BC production. Negative effects of salts could not be excluded and the osmotolerance of Gluconacetobacter xylinus needs to be further investigated in the future. Combinations of detoxification methods that efficiently decrease the concentration of inhibitors remain as an interesting option.
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| 28. |
- Guo, Xiang, et al.
(author)
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Production of bacterial nanocellulose and enzyme from [AMIM]Cl-pretreated waste cotton fabrics : effects of dyes on enzymatic saccharification and nanocellulose production
- 2016
-
In: Journal of chemical technology and biotechnology (1986). - : Wiley. - 0268-2575 .- 1097-4660. ; 91:5, s. 1413-1421
-
Journal article (peer-reviewed)abstract
- BACKGROUND Dyed used cotton textiles is a waste material associated with environmental problems. In this study, waste dyed cotton fabrics were used as feedstock for production of bacterial nanocellulose (BNC) with Gluconacetobacter xylinus and production of enzymes with Trichoderma reesei via enzymatic saccharification.RESULTS Reactive dyes caused almost no inhibition of the cellulase activity at a concentration of 5 g L-1, but decreased the BNC production at concentrations higher than 1 g L-1. The BNC yield reached 12.8 g L-1 with cotton hydrolysate, which was 48% higher than with glucose-based medium. The spent fermentation broth after BNC harvest was subsequently utilized for enzyme production. Cellulase activities produced by T. reesei reached 5.3 U mL(-1) with spent detoxified purple bed sheet (PBS) hydrolysate, and 8.2 U mL(-1) with 2-fold diluted spent PBS hydrolysate, which was almost the same or higher than with glucose medium (5.6 U mL(-1)). The xylanase activities (60.2 U mL(-1) and 88.0 U mL(-1)) obtained with the two media were 3-4 times higher than that obtained with glucose medium (21.0 U mL(-1)).CONCLUSION This approach could contribute to economical conversion of cellulosic waste to two high value-added microbial products, while also providing new raw materials for a more sustainable textile industry.
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| 29. |
- Haghighi, Mona, et al.
(author)
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A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study
- 2016
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
-
Journal article (peer-reviewed)abstract
- Regression models are extensively used in many epidemiological studies to understand the linkage between specific outcomes of interest and their risk factors. However, regression models in general examine the average effects of the risk factors and ignore subgroups with different risk profiles. As a result, interventions are often geared towards the average member of the population, without consideration of the special health needs of different subgroups within the population. This paper demonstrates the value of using rule-based analysis methods that can identify subgroups with heterogeneous risk profiles in a population without imposing assumptions on the subgroups or method. The rules define the risk pattern of subsets of individuals by not only considering the interactions between the risk factors but also their ranges. We compared the rule-based analysis results with the results from a logistic regression model in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Both methods detected a similar suite of risk factors, but the rule-based analysis was superior at detecting multiple interactions between the risk factors that characterize the subgroups. A further investigation of the particular characteristics of each subgroup may detect the special health needs of the subgroup and lead to tailored interventions.
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| 30. |
- He, Li, et al.
(author)
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Evolutionary origin and establishment of a dioecious diploid-tetraploid complex
- 2023
-
In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:11, s. 2732-2749
-
Journal article (peer-reviewed)abstract
- Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.
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| 31. |
- He, Shu-Lan, et al.
(author)
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Mitochondrial-related gene expression profiles suggest an important role of PGC-1alpha in the compensatory mechanism of endemic dilated cardiomyopathy.
- 2013
-
In: Experimental Cell Research. - : Elsevier. - 0014-4827 .- 1090-2422. ; 319:17, s. 2604-2616
-
Journal article (peer-reviewed)abstract
- Keshan disease (KD) is an endemic dilated cardiomyopathy with unclear etiology. In this study, we compared mitochondrial-related gene expression profiles of peripheral blood mononuclear cells (PBMCs) derived from 16 KD patients and 16 normal controls in KD areas. Total RNA was isolated, amplified, labeled and hybridized to Agilent human 4 × 44k whole genome microarrays. Mitochondrial-related genes were screened out by the Third-Generation Human Mitochondria-Focused cDNA Microarray (hMitChip3). Quantitative real-time PCR, immunohistochemical and biochemical parameters related mitochondrial metabolism were conducted to validate our microarray results. In KD samples, 34 up-regulated genes (ratios ≥ 2.0) were detected by significance analysis of microarrays and ingenuity systems pathway analysis (IPA). The highest ranked molecular and cellular functions of the differentially regulated genes were closely related to amino acid metabolism, free radical scavenging, carbohydrate metabolism, and energy production. Using IPA, 40 significant pathways and four significant networks, involved mainly in apoptosis, mitochondrion dysfunction, and nuclear receptor signaling were identified. Based on our results, we suggest that PGC-1alpha regulated energy metabolism and anti-apoptosis might play an important role in the compensatory mechanism of KD. Our results may lead to the identification of potential diagnostic biomarkers for KD in PBMCs, and may help to understand the pathogenesis of KD.
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| 32. |
- He, Tao, et al.
(author)
-
Kinetically Controlled Reticular Assembly of a Chemically Stable Mesoporous Ni(II)-Pyrazolate Metal-Organic Framework
- 2020
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:31, s. 13491-13499
-
Journal article (peer-reviewed)abstract
- The application scope of metal-organic frameworks (MOFs) is severely restricted by their weak chemical stability and limited pore size. A robust MOF with large mesopores is highly desired, yet poses a great synthetic challenge. Herein, two chemically stable Ni(II)-pyrazolate MOFs, BUT-32 and -33, were constructed from a conformation-matched elongated pyrazolate ligand through the isoreticular expansion. The two MOFs share the same sodalite-type net, but have different pore sizes due to the network interpenetration in BUT-32. Controlled syntheses of the two MOFs have been achieved through precisely tuning reaction conditions, where the microporous BUT-32 was demonstrated to be a thermodynamically stable product while the mesoporous BUT-33 is kinetically favored. To date, BUT-32 represents the first example of Ni-4-pyrazolate MOF whose structure was unambiguously determined by single-crystal X-ray diffraction. Interestingly, the kinetic product BUT-33 integrates 2.6 nm large mesopores with accessible Ni(II) active sites and remarkable chemical stability even in 4 M NaOH aqueous solution and 1 M Grignard reagent. This MOF thus demonstrated an excellent catalytic performance in carbon-carbon coupling reactions, superior to other Ni(II)-MOFs including BUT-32. These findings highlight the importance of kinetic control in the reticular synthesis of mesoporous MOFs, as well as their superiority in heterogeneous catalysis.
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| 33. |
- Hong, Feng, et al.
(author)
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Bacterial cellulose production from cotton-based waste textiles : enzymatic saccharification enhanced by ionic liquid pretreatment
- 2012
-
In: Bioresource Technology. - Oxford : Elsevier. - 0960-8524 .- 1873-2976. ; 104, s. 503-508
-
Journal article (peer-reviewed)abstract
- Cotton-based waste textiles were explored as alternative feedstock for production of bacterial cellulose (BC) by Gluconacetobacter xylinus. The cellulosic fabrics were treated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride ([AMIM]Cl). [AMIM]Cl caused 25% inactivation of cellulase activity at a concentration as low as of 0.02 g/mL and decreased BC production during fermentation when present in concentrations higher than 0.0005 g/mL. Therefore, removal of residual IL by washing with hot water was highly beneficial to enzymatic saccharification as well as BC production. IL-treated fabrics exhibited a 5-7-fold higher enzymatic hydrolysis rate and gave a seven times larger yield of fermentable sugars than untreated fabrics. BC from cotton cloth hydrolysate was obtained at an yield of 10.8 g/L which was 83% higher than that from the culture grown on glucose-based medium. The BC from G. xylinus grown on IL-treated fabric hydrolysate had a 79% higher tensile strength than BC from glucose-based culture medium which suggests that waste cotton pretreated with [AMIM]Cl has potential to serve as a high-quality carbon source for BC production.
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| 34. |
- Huang, Joyce Y., et al.
(author)
-
Circulating markers of cellular immune activation in prediagnostic blood sample and lung cancer risk in the Lung Cancer Cohort Consortium (LC3)
- 2020
-
In: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 146:9, s. 2394-2405
-
Journal article (peer-reviewed)abstract
- Cell-mediated immune suppression may play an important role in lung carcinogenesis. We investigated the associations for circulating levels of tryptophan, kynurenine, kynurenine:tryptophan ratio (KTR), quinolinic acid (QA) and neopterin as markers of immune regulation and inflammation with lung cancer risk in 5,364 smoking-matched case-control pairs from 20 prospective cohorts included in the international Lung Cancer Cohort Consortium. All biomarkers were quantified by mass spectrometry-based methods in serum/plasma samples collected on average 6 years before lung cancer diagnosis. Odds ratios (ORs) and 95% confidence intervals (CIs) for lung cancer associated with individual biomarkers were calculated using conditional logistic regression with adjustment for circulating cotinine. Compared to the lowest quintile, the highest quintiles of kynurenine, KTR, QA and neopterin were associated with a 20-30% higher risk, and tryptophan with a 15% lower risk of lung cancer (all p(trend) < 0.05). The strongest associations were seen for current smokers, where the adjusted ORs (95% CIs) of lung cancer for the highest quintile of KTR, QA and neopterin were 1.42 (1.15-1.75), 1.42 (1.14-1.76) and 1.45 (1.13-1.86), respectively. A stronger association was also seen for KTR and QA with risk of lung squamous cell carcinoma followed by adenocarcinoma, and for lung cancer diagnosed within the first 2 years after blood draw. This study demonstrated that components of the tryptophan-kynurenine pathway with immunomodulatory effects are associated with risk of lung cancer overall, especially for current smokers. Further research is needed to evaluate the role of these biomarkers in lung carcinogenesis and progression.
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| 35. |
- Huang, Xiao-Yu, et al.
(author)
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Matrix Factorization for Evolution Data
- 2014
-
In: Mathematical problems in engineering (Print). - : Hindawi Limited. - 1024-123X .- 1563-5147. ; , s. 525398-
-
Journal article (peer-reviewed)abstract
- We study a matrix factorization problem, that is, to find two factor matrices U and V such that R approximate to U-T x V, where R is a matrix composed of the values of the objects O-1, O-2, ... , O-n at consecutive time points T-1, T-2, ... , T-t. We first present MAFED, a constrained optimization model for this problem, which straightforwardly performs factorization on R. Then based on the interplay of the data in U,V, and R, a probabilistic graphical model using the same optimization objects is constructed, in which structural dependencies of the data in these matrices are revealed. Finally, we present a fitting algorithm to solve the proposed MAFED model, which produces the desired factorization. Empirical studies on real-world datasets demonstrate that our approach outperforms the state-of-the-art comparison algorithms.
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| 36. |
- Huang, Xiao-Yu, et al.
(author)
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Multi-Matrices Factorization with Application to Missing Sensor Data Imputation
- 2013
-
In: Sensors. - : MDPI AG. - 1424-8220. ; 13:11, s. 15172-15186
-
Journal article (peer-reviewed)abstract
- We formulate a multi-matrices factorization model (MMF) for the missing sensor data estimation problem. The estimation problem is adequately transformed into a matrix completion one. With MMF, an n-by-t real matrix, R, is adopted to represent the data collected by mobile sensors from n areas at the time, T-1, T-2, . . . , T-t, where the entry, R-i,R-j, is the aggregate value of the data collected in the ith area at T-j. We propose to approximate R by seeking a family of d-by-n probabilistic spatial feature matrices, U-(1), U-(2), . . . , U-(t), and a probabilistic temporal feature matrix, V epsilon R-dxt, where R-j approximate to U-(j)(T) T-j. We also present a solution algorithm to the proposed model. We evaluate MMF with synthetic data and a real-world sensor dataset extensively. Experimental results demonstrate that our approach outperforms the state-of-the-art comparison algorithms.
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| 37. |
- Jiang, Pengfei, et al.
(author)
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VLBI detection of the AE Aqr twin, LAMOST J024048.51+195226.9
- 2024
-
In: Monthly Notices of the Royal Astronomical Society: Letters. - 1745-3925 .- 1745-3933. ; 528:1, s. L112-L116
-
Journal article (peer-reviewed)abstract
- LAMOST J024048.51+195226.9 (J0240+1952) was recently identified as the second AE Aquarii (AE Aqr)-type cataclysmic variable, possessing the fastest known rotating white dwarf. We performed a Very Long Baseline Interferometry (VLBI) observation of J0240+1952 utilizing the European VLBI Network at 1.7 GHz, to obtain the first view of the radio morphology on mas scale. Our high-resolution VLBI image clearly shows that the radio emission is compact on mas scale (≲2 AU), with no evidence for a radio jet or extended emission. The compact radio source has an average flux density of ∼0.37 mJy, and its brightness temperature is given at ∼2.3 × 107 K, confirming a non-thermal origin. The emission exhibits irregular variations on a time-scale of tens of minutes, similar to the radio flares seen in AE Aqr. The measured VLBI position of J0240+1952 is consistent with that derived from Gaia. Our results favour the model in which the radio emission is attributed to a superposition of synchrotron radiation from expanding magnetized blobs of this system.
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| 38. |
- Jiang, Ying, et al.
(author)
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Secular Difference in Body Mass Index From 2014 to 2020 in Chinese Older Adults : A Time-Series Cross-Sectional Study
- 2022
-
In: Frontiers in Nutrition. - : Frontiers Media SA. - 2296-861X. ; 9
-
Journal article (peer-reviewed)abstract
- Background: Body mass index (BMI) is the most widely used parameter to assess the body weight status. Both the increase of BMI (overweight and obesity) and decrease of BMI (underweight) has been associated with high risk of adverse outcome, such as stroke, disability, and even death. However, recent data on secular differences in BMI in the Chinese aged population are limited. The present study provides robust new evidence about the evolving epidemic of obesity among aged adults in China.Objective: Evaluating secular difference in BMI in a group of Chinese older adults.Materials and Methods: We analyzed 7 continuous survey years (2014–2020), including 50,192 Chinese aged participants (25,505 men and 24,687 women, aged 71.9 ± 6.1 years, age range: 65–99 years). Information on sex, age, height, and body weight, was collected based on medical history. Participants were classified into four groups: underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 25 kg/m2), overweight (25 kg/m2 ≤ BMI < 30 kg/m2), and obesity (BMI ≥ 30 kg/m2). Linear regressions were used to assess the secular difference in BMI. Sex and age differences were also evaluated by stratified analyses.Results: From 2014 to 2020, age-adjusted mean BMI increased by 0.3 kg/m2 (95% CI: 0.1, 0.5 kg/m2) in men, and 0.5 kg/m2 (95% CI: 0.2, 0.7 kg/m2) in women. Age-standardized prevalence of underweight decreased from 3.0 to 2.3% in men, and from 3.0 to 2.1% in women. Age-standardized prevalence of overweight increased in both men (from 40.1 to 41.7%) and women (from 37.8 to 39.8%), and so as obesity (men: from 4.1 to 6.1%; women: from 5.8 to 8.7%).Conclusion: Our results confirmed that BMI gradually increased from 2014 to 2020. The age-adjusted mean BMI increased by 0.3 kg/m2 in older men, and 0.5 kg/m2 in older women. The age- and sex-standardized prevalence of overweight and obesity significantly increased, especially in 70–79-year age group, while the prevalence of underweight decreased. The combination of a balanced-diet and physical exercise is needed to maintain optimal BMI range for the aged population.
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| 39. |
- Kato, Norihiro, et al.
(author)
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Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
- 2015
-
In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 47:11, s. 1282-1293
-
Journal article (peer-reviewed)abstract
- We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10−11 to 5.0 × 10−21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10−6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.
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| 40. |
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| 41. |
- Li, Junjie, et al.
(author)
-
A Novel Dry Selective Isotropic Atomic Layer Etching of SiGe for Manufacturing Vertical Nanowire Array with Diameter Less than 20 nm
- 2020
-
In: Materials. - : MDPI AG. - 1996-1944. ; 13:3
-
Journal article (peer-reviewed)abstract
- Semiconductor nanowires have great application prospects in field effect transistors and sensors. In this study, the process and challenges of manufacturing vertical SiGe/Si nanowire array by using the conventional lithography and novel dry atomic layer etching technology. The final results demonstrate that vertical nanowires with a diameter less than 20 nm can be obtained. The diameter of nanowires is adjustable with an accuracy error less than 0.3 nm. This technology provides a new way for advanced 3D transistors and sensors.
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| 42. |
- Li, Jian Feng, et al.
(author)
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Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases
- 2018
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 115:50, s. 11711-11720
-
Journal article (peer-reviewed)abstract
- Most B cell precursor acute lymphoblastic leukemia (BCP ALL) can be classified into known major genetic subtypes, while a substantial proportion of BCP ALL remains poorly characterized in relation to its underlying genomic abnormalities. We therefore initiated a large-scale international study to reanalyze and delineate the transcriptome landscape of 1,223 BCP ALL cases using RNA sequencing. Fourteen BCP ALL gene expression subgroups (G1 to G14) were identified. Apart from extending eight previously described subgroups (G1 to G8 associated with MEF2D fusions, TCF3–PBX1 fusions, ETV6–RUNX1–positive/ETV6–RUNX1–like, DUX4 fusions, ZNF384 fusions, BCR–ABL1/Ph–like, high hyperdiploidy, and KMT2A fusions), we defined six additional gene expression subgroups: G9 was associated with both PAX5 and CRLF2 fusions; G10 and G11 with mutations in PAX5 (p.P80R) and IKZF1 (p.N159Y), respectively; G12 with IGH–CEBPE fusion and mutations in ZEB2 (p.H1038R); and G13 and G14 with TCF3/4–HLF and NUTM1 fusions, respectively. In pediatric BCP ALL, subgroups G2 to G5 and G7 (51 to 65/67 chromosomes) were associated with low-risk, G7 (with ≤50 chromosomes) and G9 were intermediate-risk, whereas G1, G6, and G8 were defined as high-risk subgroups. In adult BCP ALL, G1, G2, G6, and G8 were associated with high risk, while G4, G5, and G7 had relatively favorable outcomes. This large-scale transcriptome sequence analysis of BCP ALL revealed distinct molecular subgroups that reflect discrete pathways of BCP ALL, informing disease classification and prognostic stratification. The combined results strongly advocate that RNA sequencing be introduced into the clinical diagnostic workup of BCP ALL. four decades, most of the recurring chromosomal abnormalities, including aneuploidy, chromosomal rearrangements/gene fusions (e.g., ETV6–RUNX1, BCR–ABL1, and TCF3–PBX1), and rearrangements of KMT2A (previously MLL), were identified by.
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| 43. |
- Liu, Si, et al.
(author)
-
Ligand modification to stabilize the cobalt complexes for water oxidation
- 2017
-
In: International journal of hydrogen energy. - : Elsevier. - 0360-3199 .- 1879-3487. ; 42:50, s. 29716-29724
-
Journal article (peer-reviewed)abstract
- Ligand modifications with electron-withdrawing and electron-donating groups were applied to afford three novel mononuclear cobalt-based catalysts [Co(TPA-R)]2+ (TPA = tris(2-pyridylmethyl) amine; R = tri-α F, 1; R = tri-αOMe, 2; R = mono-αF, 3) for water oxidation. Characterization of the catalysts shows that steric and electronic factors play important roles in inhibiting spontaneous intermolecular dimerization of two cobalt centers, and influence the catalytic behavior. Complex 1 exhibits the best catalytic ability and stability, showing a good efficiency with TOF of 6.03 ± 0.02 mol (O2)/(mol (cat)*s) in photo-induced water oxidation experiments using Ru (bpy)3 2+ as photosensitizer and Na2S2O8 as electron acceptor. The bulky electron donating groups in 2 led to degradation of the complex and formation of CoOx particles acting as the real catalyst. Electron-withdrawing substituents on the TPA ligand can stabilize the catalyst under both electrochemical and photo-induced conditions, with the enhancement increasing with the number of the electron-withdrawing groups. © 2017 Hydrogen Energy Publications LLC.
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| 44. |
- Liu, Xuan, et al.
(author)
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Increased southerly and easterly water vapor transport contributed to the dry-to-wet transition of summer precipitation over the Three-River Headwaters in the Tibetan Plateau
- 2023
-
In: Advances in Climate Change Research. - 1674-9278 .- 2524-1761. ; 14:4, s. 502-510
-
Journal article (peer-reviewed)abstract
- The Three-River Headwaters (TRH) region in the Tibetan Plateau is vulnerable to climate change; changes in summer (June–August) precipitation have a significant impact on water security and sustainability in both local and downstream areas. However, the changes in summer precipitation of different intensities over the TRH region, along with their influencing factors, remain unclear. In this study, we used observational and ERA5 reanalysis data and employed a precipitation categorization and water vapor budget analysis to quantify the categorized precipitation variations and investigate their possible linkages with the water vapor budget. Our results showed an increasing trend in summer precipitation at a rate of 0.9 mm per year (p < 0.1) during 1979–2020, with a significant dry-to-wet transition in 2002. The category ‘very heavy precipitation’ (≥10 mm d−1) contributed 65.1% of the increased summer precipitation, which occurred frequently in the northern TRH region. The dry-to-wet transition was caused by the effects of varied atmospheric circulations in each subregion. Southwesterly water vapor transport through the southern boundary was responsible for the increased net water vapor flux in the western TRH region (158.2%), while southeasterly water vapor transport through the eastern boundary was responsible for the increased net water vapor flux in the central TRH (155.2%) and eastern TRH (229.2%) regions. Therefore, we inferred that the dry-to-wet transition of summer precipitation and the increased ‘very heavy precipitation’ over the TRH was caused by increased easterly and southerly water vapor transport.
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| 45. |
- Lixing, Zhou, et al.
(author)
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Understanding dipole formation at dielectric/dielectric hetero-interface
- 2018
-
In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 113:18
-
Journal article (peer-reviewed)abstract
- Band alignment and dipole formation at the hetero-interface still remain fascinating and, hence, are being intensively investigated. In this study, we experimentally investigate the dipole formation by employing a dielectric/dielectric (Al2O3/GeO2) interface. We investigate the dipole dependence on various post-deposition annealing (PDA) ambiences from the viewpoints of electrical extraction and the X-ray photoelectron spectroscopy measurement. The core level shift at the Al2O3/GeO2 interface is consistent with the dipole changes in various PDA ambiences. We discover that the dipole formation can be well explained by the interface gap state and charge neutrality level theory. These results further confirm the feasibility of gap state theory in explaining the band alignment at hetero-junctions. This study can be a booster to enhance the comprehension of dipole origin at hetero-junction interfaces.
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| 46. |
- Lu, Yingchang, et al.
(author)
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Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
- 2020
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In: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 29:2, s. 477-486
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Journal article (peer-reviewed)abstract
- Background: Risk variants identified so far for colorectal cancer explain only a small proportion of milial risk of this cancer, particularly in Asians.Methods: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, cluding 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 omising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls European descent. To identify additional risk variants in known colorectal cancer loci, we performed nditional analyses in East Asians.Results: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk P = 3.9 x 10(-8) in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This sociation was replicated in European descendants using a variant (rs2938616) in complete linkage sequilibrium with rs67052019 (P = 7.7 x 10(-3)). Of the remaining 59 variants, 12 showed an association P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 x 10(-8) and o variants with an association near the genome-wide significance level (rs60911071, P = 5.8 x 10(-8); 62558833, P = 7.5 x 10(-8)) in the combined analyses of Asian- and European-ancestry data. In addition, ing data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS.Conclusions: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for lorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the iology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal ncer risk loci identified previously.Impact: Our study provides novel data to improve the understanding of the genetic basis for colorectal ncer risk.
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| 47. |
- Qin, Changliang, et al.
(author)
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Process optimizations to recessed e-SiGe source/drain for performance enhancement in 22 nm all-last high-k/metal-gate pMOSFETs
- 2016
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In: Solid-State Electronics. - : Elsevier. - 0038-1101 .- 1879-2405. ; 123, s. 38-43
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Journal article (peer-reviewed)abstract
- In this paper, the technology of recessed embedded SiGe (e-SiGe) source/drain (S/D) module is optimized for the performance enhancement in 22 nm all-last high-k/metal-gate (HK/MG) pMOSFETs. Different Si recess-etch techniques were applied in S/D regions to increase the strain in the channel and subsequently, improve the performance of transistors. A new recess-etch method consists of a two-step etch method is proposed. This process is an initial anisotropic etch for the formation of shallow trench followed by a final isotropic etch. By introducing the definition of the upper edge distance (D) between the recessed S/D region and the channel region, the process advantage of the new approach is clearly presented. It decreases the value of D than those by conventional one-step isotropic or anisotropic etch of Si. Therefore, the series resistance is reduced and the channel strain is increased, which confirmed by the simulation results. The physical reason of D reducing is analyzed in brief. Applying this recess design, the implant conditions for S/D extension (SDE) are also optimized by using a two-step implantation of BF2 in SiGe layers. The overlap space between doping junction and channel region has great effect on the device's performance. The designed implantation profile decreases the overlap space while keeps a shallow junction depth for a controllable short channel effect. The channel resistance as well as the transfer ID-VG curves varying with different process conditions are demonstrated. It shows the drive current of the device with the optimized SDE implant condition and Si recess-etch process is obviously improved. The change trend of on-off current distributions extracted from a series of devices confirmed the conclusions. This study provides a useful guideline for developing high performance strained PMOS SiGe technology.
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| 48. |
- Radamson, Henry H., et al.
(author)
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Miniaturization of CMOS
- 2019
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In: Micromachines. - : MDPI AG. - 2072-666X. ; 10:5
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Journal article (peer-reviewed)abstract
- When the international technology roadmap of semiconductors (ITRS) started almost five decades ago, the metal oxide effect transistor (MOSFET) as units in integrated circuits (IC) continuously miniaturized. The transistor structure has radically changed from its original planar 2D architecture to today's 3D Fin field-effect transistors (FinFETs) along with new designs for gate and source/drain regions and applying strain engineering. This article presents how the MOSFET structure and process have been changed (or modified) to follow the More Moore strategy. A focus has been on methodologies, challenges, and difficulties when ITRS approaches the end. The discussions extend to new channel materials beyond the Moore era.
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| 49. |
- Radamson, Henry H., et al.
(author)
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State of the Art and Future Perspectives in Advanced CMOS Technology
- 2020
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In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:8
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Research review (peer-reviewed)abstract
- The international technology roadmap of semiconductors (ITRS) is approaching the historical end point and we observe that the semiconductor industry is driving complementary metal oxide semiconductor (CMOS) further towards unknown zones. Today's transistors with 3D structure and integrated advanced strain engineering differ radically from the original planar 2D ones due to the scaling down of the gate and source/drain regions according to Moore's law. This article presents a review of new architectures, simulation methods, and process technology for nano-scale transistors on the approach to the end of ITRS technology. The discussions cover innovative methods, challenges and difficulties in device processing, as well as new metrology techniques that may appear in the near future.
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| 50. |
- Ren, Luyao, et al.
(author)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Journal article (peer-reviewed)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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